9H0M | pdb_00009h0m

Structure of avian Pit54 SRCR 1-2 in complex with hemoglobin

PDB DOI: https://doi.org/10.2210/pdb9H0M/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Gallus gallus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2024-10-08 Released: 2025-10-29
Deposition Author(s): Mikkelsen, J.H., Andersen, C.B.F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.201 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Models: in silico, experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of avian Pit54 SRCR 1-2 in complex with hemoglobin

Mikkelsen, J.H., Andersen, C.B.F.

To be published.

Macromolecule Content

Total Structure Weight: 354.48 kDa
Atom Count: 15,794
Modeled Residue Count: 2,000
Deposited Residue Count: 3,188
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-A	A, C, G, I	142	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P01994 (Gallus gallus) Explore P01994 Go to UniProtKB: P01994
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01994
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D, H, J	147	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P02112 (Gallus gallus) Explore P02112 Go to UniProtKB: P02112
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02112
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PIT54 protein	E, F, K, L	508	Gallus gallus	Mutation(s): 0 Gene Names: PIT54
UniProt
Find proteins for A0A8V0XEL0 (Gallus gallus) Explore A0A8V0XEL0 Go to UniProtKB: A0A8V0XEL0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8V0XEL0
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E Focus chain F Focus chain K
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	M, N	4		N-Glycosylation	Interactions Focus chain M Focus chain N Interactions & Density Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	2		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain X [auth G] SDF format, chain Y [auth H] SDF format, chain Z [auth I] MOL2 format, chain AA [auth J] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth I] mmCIF format, chain AA [auth J] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth H] mmCIF format, chain Z [auth I]	AA [auth J] P [auth A] Q [auth B] R [auth C] S [auth D] AA [auth J], P [auth A], Q [auth B], R [auth C], S [auth D], X [auth G], Y [auth H], Z [auth I]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth J] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth K] SDF format, chain CA [auth K] SDF format, chain DA [auth L] SDF format, chain EA [auth L] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] MOL2 format, chain BA [auth K] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth L] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] mmCIF format, chain BA [auth K] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth L] mmCIF format, chain EA [auth L] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F]	BA [auth K] CA [auth K] DA [auth L] EA [auth L] T [auth E] BA [auth K], CA [auth K], DA [auth L], EA [auth L], T [auth E], U [auth E], V [auth F], W [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth K] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain BA [auth K] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F]